Non-Standard Residue

Any residue of protein or nucleic acid that is not included in the list of Standard Residues is considered Non-Standard. The atomic coordinates for atoms in non-standard residues are given in records of type HETATM in the PDB file format.

Examples:


 * SEP and TPO in 1bkx
 * 1MA, 2MG, 5MC, 5MU, 7MG, H2U, M2G, OMC, OMG, PSU, and YG in 1evv
 * PSU and several others in tRNA
 * MSE in 2ab5

Although phosphoserine and phosphothreonine are given as non-standard residues SEP and TPO in 1bkx, an alternative convention may also be followed.

For example, a non-standard phenylethane amino acid sidechain in 1b07 is named GLY (GLY 5 on chain C in ATOM records) plus PYL (sequence number 1005 in chain C in HETATM records).

The former scheme of designating modified standard nucleotides with plus signs (+A, +C, +G, +I, +T, +U) was discontinued in the PDB remediation project, effective August 1, 2007. The unremdiated files can still be obtained, see Getting Unremediated PDB Files.